Welcome to the Community, @DBromley. I'm here to provide some details about managing cash deposits in QuickBooks Self-Employed (QBSE).
I appreciate you sharing detailed info about your concern. To help you with this, you can create an invoice in your QBSE account if you've issued one to your customers. You can then categorise the deposit as business income in the banking section. You do not need to create the invoice unless you would like to send it/keep it for your business records.
I also recommend reaching out to your accountant for additional guidance in managing the transactions. This is to ensure you'll record them correctly to avoid messing up your books.
The program also allows you to make rules to categorise recent and past transactions quickly. To get started, please visit this link for detailed steps: Create rules to speed up reviews in QuickBooks Self-Employed.
Please post again here if you have any other concerns about managing cash deposits in QuickBooks. I'll be more than happy to lend a hand. Have a good one and take care.
